ABSTRACT
Among the most important achievements of molecular evolutionary genetics is the discovery of the approximate constancy of the rate of amino acid or nucleotide substitution. This discovery gave us a new tool for phylogenetic tree construction. As stressed in Chapter 4, the steady rate of amino acid or nucleotide substitution holds only approximately, and there are some assumptions and complications. That is why reconstruction of a phylogeny and estimation of divergence time require a professional approach and knowledge of the whole complexity of the matter studied. However, compared with morphological or paleontological approaches, molecular data exhibit more reproducible patterns of evolutionary change. Molecular divergence may be measured in a single, comparative scale, as we summarized in Chapters 1 and 7. Consequently this can provide comparative values, and permit us to evaluate genealogy on the quantitative genetic basis of estimated co-ancestry, unlike with morphological and paleontological data, where there are many experts’ inferences. Therefore, molecular phylogenetic approaches may give clearer representation of evolutionary relationship of organisms than, say, morphological characters. For a tree built on the basis of morphological traits, it is very diffi cult to give an evolutionary time scale. On the contrary, it is easy to convert molecular divergence into time estimates. This knowledge led to formation of the new fi eld of genetics and evolutionary biology that is Molecular Phylogenetics. A very important property, which some critics of molecular phylogenetics do not comprehend (Pavlinov 2005), is that genes and genomes are transmitted through gender lines or via germ-plasm without environmental modifi cations and thus comprising a real basis for homology-orthology estimates of traits for the reconstruction of phylogeny. All this does not mean that other approaches should be rejected as outdated. The complexity of life, species types and modes of their evolution means that no single approach will always work, even the most modern approaches. This understanding was evident when trees based on allozymes and morphology together predicted relationships in some cases better (more explanatory in a complex background) than simple molecular genetic approaches (Hillis et al. 1996; Avise and Wollenberg 1997).
